Thursday, July 2, 2015

Variants of peer review

In my field of science, peer review generally takes the following form: You submit a manuscript to a journal, it is reviewed by two to three colleagues, and then the editor of the journal decides whether to publish, whether to request changes before re-examining the paper for publication, or whether to reject. The editor and the peer reviewers know who wrote the paper, but you don't usually know who the reviewers were.

There are other ways of doing this; they have their own advantages and disadvantages, but I definitely know how I would change things if I could.

One often heard suggestion lately is that peer review should be "open" (or public); that is, the authors should be informed who the reviewers were. As far as I can see, there are two main considerations behind this. First, that this will make it harder to be unfair and rude, which is of course much easier to be under our current system. Second, a general and in this particular case unwarranted infatuation with the concept of openness, as in open source software or open access publishing.

Because there is one very simple problem: If the author can see who suggested their paper be rejected, will that not have a severely chilling effect? Imagine a postdoc reviewing the manuscript of a very influential professor, for example. Will they dare to say something negative if they know their name will be connected with it, be it ever so justified? I am fairly sure that I at least would say no considerably more often if I were to asked to review papers under an open system. Who knows when I would offend somebody who has to decide about my grant application a year later?

Wednesday, July 1, 2015

Botany picture #205: Coprosma hirtella

Wanted to write something, but too tired now. Instead: Coprosma hirtella (Rubiaceae), Australian Capital Territory, 2015. Again, as a German one gets a very lopsided view of the Rubiaceae family because it is mostly represented in Europe with scraggly herbs bearing pseudo-verticllate leaves. Most species of the family, which by the way is one of the ten largest flowering plant families, are actually woody and have opposite leaves.

This is from our little day trip to Mount Franklin Road in Namadgi National Park in late summer, the same where we saw the Royal Bluebell.

Monday, June 29, 2015

Panbiogeography once more: relatedness between biota, parsimony of dispersal events, and the garden of Eden

For some reason, the first author of Nelson & Ladiges (2001), Gondwana, vicariance biogeography and the New York School revisited, recently sent me that paper with the comment "an item of possible interest". I can only assume that this is because I was anti-convinced that panbiogeography makes sense by the recent contributions of Michael Heads to Australian Systematic Botany.

(Anti-convinced meaning here that not only did they fail to convince me of the virtues of the approach, but the circularity of the first paper's example analysis actually pushed me further towards considering panbiogeography to be unscientific than I was before reading it.)

I always find it interesting to consider arguments challenging my position, but I am not entirely sure how Nelson & Ladiges (2001) is relevant to Heads (2015). The logic of the 2001 paper is rather different from Heads' recent argumentation, and its methodology is rather different from his demonstrative example of a panbiogeographic analysis, so even if I would say "hey, makes sense" after reading it that would still not help the circularity of Heads' analytic approach.

Still, reading it was very insightful; I only now fully appreciate that certain schools of thought appear to be interested not primarily in reconstructing the ancestral areas and movements of lineages (as Heads seemed to be in his recent papers) or in bioregionalisation, but in reconstructing relationships between biota. They try to arrive at something like a phylogenetic tree of biota, where one can say, for example, that the "boreal" region is the sister of the "austral" region.

I find this very remarkable, for several unrelated reasons.

Saturday, June 27, 2015

Science spam the umpteenth

Just when I thought spam mails from for-profit "journals" had gotten a bit more professional looking lately, I get this:

If trying to look like a serious scientific publication is here, then the above spam message is... somewhere outside the local group of galaxies, I think?

As for the claim that indexed journals are often considered to be higher quality than non-indexed ones, that is true as far as it goes. Unfortunately, Google Scholar is not really a selective indexing service but a search engine, and I have never heard of any of the others.

Wednesday, June 24, 2015

Fun with scientific plant names

Long time no blog; not enough ideas what to write, too much else to do.

Just went through a big dataset of Asteraceae (daisy or sunflower family, also known as Compositae), and I realised how many silly scientific genus names there are. Some of the highlights:

Pseudobahia, Pseudoclappia, Pseudoconyza, Pseudohandelia, Pseudonoseris, and Pseudostifftia are, of course, all based on similarity to genera with exactly the same names only without the Pseudo-.

Similarly, I feel that Senecio, Dendrosenecio, Nemosenecio, Parasenecio and Sinosenecio betray a certain, let us say, lack of imagination in naming members of the Senecioneae tribe.

Erato sounds odd but was apparently one of the Ancient Greek Muses. No idea whether the genus Oblivia has a similarly defensible etymology though.

Damnxanthodium is perhaps the best. Xantho- means yellow, and as can be imagined 'damn' is neither Ancient Greek nor Latin. It is an obvious reference to the American abbreviation DYC, which stands for Damn Yellow Composite, in other words the complaint about so many of them looking pretty much alike. A zoologist counterpart is apparently LBB for Little Brown Bird.

Friday, June 19, 2015

Botany picture #204: Cassinia arcuata

Admittedly Cassinia arcuata (Asteraceae) cannot be counted among the prettiest members of the sunflower family, and despite being native to Australia it is actually a declared noxious weed in the state of New South Wales. Still, it is an interesting plant. As a shrub with large numbers of brownish, few-flowered flower-heads - I can only assume it is wind-pollinated? - and apparently able to quickly come up after fires it has an interesting ecology. It is also strongly aromatic.

The specimen in the picture is part of plantings in the Southern Tablelands Ecosystems Park at the National Arboretum here in Canberra.

Monday, June 15, 2015

Peer review and competing schools of thought

Peer review in science works quite well, I think, if everybody is agreed on the fundamental assumptions and the proper methodology of the field. If somebody gives me a bog standard phylogenetic or taxonomic study to review, I know what to look for, I know what should be there, and it is easy to write a report.

The problem is when the paper is from one side in a heated controversy. In my field of work, generously circumscribed as ranging from systematics across biogeography to evolutionary biology, the following come to mind:
These are not all comparable, by the way. In some cases, the truth is likely somewhere in the middle, but in others only one side can be right.

Anyway, assume you are an entirely neutral journal editor and you need to get reviewers' reports for a paper from one of those sides, let us say from a panbiogeographer doing a panbiogeographic analysis. Who do you send it to?

If you send it to a mainstream biogeographer, you already know that they are going to recommend rejection because they consider the entire methodology and its assumptions to be unscientific. The same if the roles are reversed; a colleague had a paper rejected because he found evidence for long distance dispersal and ran into a reviewer (and an editor) who don't believe that it is possible. Send it to somebody who isn't on either side? Well, they are likely not qualified to review in the first place, otherwise they would already have picked a side.

So how does such a conflict ever get resolved? Keep the two parties carefully separated and hope that one of them dies out? That is also a form of post-publication review I guess.

My perspective is currently that of having been asked to review a paper from a representative of a school of thought that looks to me kind of like this:

What to do? I informed the editor that I should be considered biased, but he wanted my opinion anyway. Having an editor who listens to both sides, takes their respective views with a grain of salt, and then makes up their own mind is probably the best one can hope for. But pre-publication peer review is still a very imperfect tool in such a situation.